On Tony Woods claim site there is a distinction made between Fortress IIs and B-17s. Am I correct in assuming that the former are RAF machines employed on Coastal Command duties while the latter are American bombers employed in, well.... bombing?

The use of "Fortress II" or "BF II" in a German report does not imply an RAF aircraft. These terms can be found in contexts (e.g. the KTB of Stab JG 77) where the Fortresses concerned are definitely American.

My guess is that the Germans became aware of the RAF designation for the B-17 before they learned the American one, it found its way into a recognition manual and some people stuck to what they knew while others later began using the USAAF designation.